Package picard.illumina
Class BarcodeExtractor
- java.lang.Object
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- picard.illumina.BarcodeExtractor
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public class BarcodeExtractor extends Object
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
BarcodeExtractor.BarcodeMatch
Utility class to hang onto data about the best match for a given barcode
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Constructor Summary
Constructors Constructor Description BarcodeExtractor(Map<String,BarcodeMetric> barcodeToMetrics, BarcodeMetric noMatchMetric, ReadStructure readStructure, int maxNoCalls, int maxMismatches, int minMismatchDelta, int minimumBaseQuality, DistanceMetric distanceMode)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static String[]
generateNoMatchBarcode(ReadStructure inputReadStructure)
Map<String,BarcodeMetric>
getMetrics()
int
getMinimumBaseQuality()
BarcodeMetric
getNoMatchMetric()
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Constructor Detail
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BarcodeExtractor
public BarcodeExtractor(Map<String,BarcodeMetric> barcodeToMetrics, BarcodeMetric noMatchMetric, ReadStructure readStructure, int maxNoCalls, int maxMismatches, int minMismatchDelta, int minimumBaseQuality, DistanceMetric distanceMode)
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Method Detail
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getMetrics
public Map<String,BarcodeMetric> getMetrics()
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getNoMatchMetric
public BarcodeMetric getNoMatchMetric()
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getMinimumBaseQuality
public int getMinimumBaseQuality()
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generateNoMatchBarcode
public static String[] generateNoMatchBarcode(ReadStructure inputReadStructure)
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